We use snakemake [@Dadasnake2021] to
maintain reproducibility and improvement of the bioinformatics analysis
of microbiome data.
Microbial Profiling Options
Classification of Operational Taxonomic Units (OTUs)
OTUs are clusters with sequence similarity and are accepted as an
analytical unit used in microbial profiling using 16S rRNA gene
markers.
Classification of Phylotype
A phylotype in microbiome research is a DNA sequence or group of
sequences sharing more than an arbitrarily chosen level of similarity of
a 16S rRNA gene marker.
Classification of Amplicon Sequence Variant (ASV)
An ASV in microbiome research is any one of the inferred single DNA
sequences recovered from a bioinformatics analysis of 16S rRNA marker
genes.
Classification of Microbiaal Phylogenies
Microbial phylogenies are estimated from gene sequences homologies
and using models of mutation to infer most-likely evolutionary
histories.